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Re: [ESPResSo-users] continue an interrupted simulation which used pepti

From: Stefan Kesselheim
Subject: Re: [ESPResSo-users] continue an interrupted simulation which used peptideB
Date: Thu, 28 Feb 2013 14:42:48 +0100

Hi Pee,

On Feb 28, 2013, at 2:35 PM, pdam bright <address@hidden> wrote:

> Dear all, 
> I am using peptideB to simulate a peptide. But my computer has been shut down 
> and I have to run it from the beginning. Is there any way to continue the 
> simulation from where it has been interrupted using the last VMD file?

In principle this might be possible, but surely is not intended that way. A 
good method for continue simulations is using the blockfile format to regularly 
store the necessary particle data (and other parameters) and write the 
simulation script in two variants: One for the initial setup and one that 
allows to continue the simulation from the data stored in a block file.
We do not support "checkpointing" in the sense that you can have an 
automatically created file that contains everything necessary to continue 
running. One reason is that this would include the necessity to store the full 
state of the TCL interpreter. 

If it is just one afternoon of computation, it is probably easier to re-run the 
simulation :-). The particle positions can however be extracted from a vtf 
file, if necessary, but that is manual work.

Cheers and good luck,

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